Piñataversity – a biodiversity assessment of Viva Piñata

Revisiting Piñata Island

Every now and then, my gaming habits tend to take a bit of a wander down memory lane. Of late, that means cracking out one of my classic faves – the life simulation and “collectathon” Viva Piñata by Rare. Originally released in 2006, with successor (expanded version, essentially) Viva Piñata: Trouble in Paradise released in 2008, the game essentially involves creating a lavish garden to attract wild piñata-like animals. Although a little light on plot, the main goal is to entice these wild creatures (Wilds) to stay in your garden (becoming Residents), to later be sent off to parties across the globe. Trouble in Paradise boasts a roster of 88 different species of Piñatas to collect, as well as a variety of fruiting trees, plants, and flowers to grow.

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Our hand in maladaptation

Maladaptation

In the previous post on The G-CAT, we talked about the role of maladaptation in the evolution of populations and species, and how this might impact their future. To summarise, maladaptation is the process (or trait responsible for) which causes a reduction in the fitness. As we discussed, this can come about a number of ways – such as from a shift in the selective environment or from fitness trade-offs in traits over time – and predominantly impacts on species by reducing their capacity to adapt. Particularly, this is important for small populations or those lacking in genetic diversity, which are already at risk of entering an extinction vortex and lack the capability to respond well to extreme selective changes (such as contemporary climate change).

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What’s yours is mine: evolution by adaptive introgression

Gene flow and introgression

Genetic variation remains a key component of not only understanding the process and history of evolution, but also for allowing evolution to continue into the future. This is the basis of the concept of ‘evolutionary potential’ – the available variation within a population or species which may enable them to adapt to new environmental stressors as they occur. With the looming threat of contemporary climate change and environmental transformations by humanity, predicting and supporting evolutionary potential across the diversity of life is critical for conserving the stability of our biosphere.

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UnConservation Genetics: tools for managing invasive species

Conservation genetics

Naturally, all species play their role in the balancing and functioning of ecosystems across the globe (even the ones we might not like all that much, personally). Persistence or extinction of ecologically important species is a critical component of the overall health and stability of an ecosystem, and thus our aim as conservation scientists is to attempt to use whatever tools we have at our disposal to conserve species. One of the most central themes in conservation ecology (and to The G-CAT, of course) is the notion that genetic information can be used to better our conservation management approaches. This usually involves understanding the genetic history and identity of our target threatened species from which we can best plan for their future. This can take the form of genetic-informed relatedness estimates for breeding programs; identifying important populations and those at risk of local extinction; or identifying evolutionarily-important new species which might hold unique adaptations that could allow them to persist in an ever-changing future.

Applications of conservation genetics.jpg
Just a few applications of genetic information in conservation management, such as in breeding programs and pedigrees (left), identifying new/cryptic species (centre) and identifying and maintaining populations and their structure (right).

The Invaders

Contrastingly, sometimes we might also use genetic information to do the exact opposite. While so many species on Earth are at risk (or have already passed over the precipice) of extinction, some have gone rogue with our intervention. These are, of course, invasive species; pests that have been introduced into new environments and, by their prolific nature, start to throw out the balance of the ecosystem. Australians will be familiar with no shortage of relevant invasive species; the most notable of which is the cane toad, Rhinella marina. However, there are a plethora of invasive species which range from notably prolific (such as the cane toad) to the seemingly mundane (such as the blackbird): so how can we possibly deal with the number and propensity of pests?

Table of invasive species in Australia
A table of some of the most prolific mammalian invasive species in Australia, including when they were first introduced and why, and their (relatively) recently estimated population sizes. Source: Wikipedia (and studies referenced therein). Some estimated numbers might not reflect current sizes as they were obtained from studies over the last 10 years.

Tools for invasive species management

There are a number of tools at our disposal for dealing with invasive species. These range from chemical controls (like pesticides), to biological controls and more recently to targeted genetic methods. Let’s take a quick foray into some of these different methods and their applications to pest control.

Types of control tools for invasive species
Some of the broad categories of invasive species control. For any given pest species, such as the cane toad (top), we might choose to use a particular set of methods to reduce their numbers. These can include biological controls (such as the ladybird, for aphid populations (left)); chemical controls such as pesticides; or even genetic engineering technologies.

Biological controls

One of the most traditional methods of pest control are biological controls. A biological control is, in simple terms, a species that can be introduced to an afflicted area to control the population of an invasive species. Usually, this is based on some form of natural co-evolution or hierarchy: species which naturally predate upon, infect or otherwise displace the pest in question are preferred. The basis of this choice is that nature, and evolution by natural selection, often creates a near-perfect machine adapted for handling the exact problem.

Biological controls can have very mixed results. In some cases, they can be relatively effective, such as the introduction of the moth Cactoblastis cactorum into Australia to control the invasive prickly pear. The moth lays eggs exclusively within the tissue of the prickly pear, and the resultant caterpillars ravish the plant. There has been no association of secondary diet items for caterpillars, suggesting the control method has been very selective and precise.

Moth biological control flow chart
The broad life cycle of the cactus moth and how it controls the invasive prickly pear in Australia. The ravenous caterpillar larvae of the moth is effective at decimating prickly pears, whilst the moth’s specificity to this host means there is limited impact on other plant species.

On the contrary, bad biological controls can lead to ecological disasters. As mentioned above, the introduction of the cane toad into Australia has been widely regarded as the origin of one of the worst invasive pests in the nation’s history. Initially, cane toads were brought over in the 1930s to predate on the (native) cane beetle, which was causing significant damage to sugar cane plantations in the tropical north. Not overly effective at actually dealing with the problem they were supposed to deal with, the cane toad rapidly spread across northern portion of the continent. Native species that attempt to predate on the cane toad often die to their defensive toxin, causing massive ecological damage to the system.

The potential secondary impact of biological controls, and the degree of unpredictability in how they will respond to a new environment (and how native species will also respond to their introduction) leads conservationists to develop new, more specific techniques. In similar ways, viral and bacterial-based controls have had limited success (although are still often proposed in conservation management, such as the planned carp herpesvirus release).

Genetic controls?

It is clear that more targeted and narrow techniques are required to effectively control pest species. At a more micro level, individual genes could be used to manage species: this is not the first way genetic modification has been proposed to deal with problem organisms. Genetic methods have been employed for years in crop farming through genetic engineering of genes to produce ‘natural’ pesticides or insecticides. In a similar vein, it has been proposed that genetic modification could be a useful tool for dealing with invasive pests and their native victims.

Gene drives

One promising targeted, genetic-based method that has shown great promise is the gene drive. Following some of the theory behind genetic engineering, gene drives are targeted suites of genes (or alleles) which, by their own selfish nature, propagate through a population at a much higher rate than other alternative genes. In conjunction with other DNA modification methods, which can create fatal or sterilising genetic variants, gene drives present the opportunity to allow the natural breeding of an invasive species to spread the detrimental modified gene.

Gene drive diagram
An example of how gene drives are being proposed to tackle malaria. In this figure, the pink mosquito at the top has been genetically engineered using CRISPR to possess two important genetic elements: a genetic variant which causes the mosquito to be unable to produce eggs or bite (the pink gene), and a linked selfish genetic element (the gene drive itself; the plus) which makes this detrimental allele spread more rapidly than by standard inheritance. Sources: Nature and The Australian Academy of Science.

Although a relatively new, and untested, technique, gene drive technology has already been proposed as a method to address some of the prolific invasive mammals of New Zealand. Naturally, there are a number of limitations and reservations for the method; similar to biological control, there is concern for secondary impact on other species that interact with the invasive host. Hybridisation between invasive and native species would cause the gene drive to be spread to native species, counteracting the conservation efforts to save natives. For example, a gene drive could not reasonably be proposed to deal with feral wild dogs in Australia without massively impacting the ‘native’ dingo.

Genes for non-genetic methods

Genetic information, more broadly, can also be useful for pest species management without necessarily directly feeding into genetic engineering methods. The various population genetic methods that we’ve explored over a number of different posts can also be applied in informing management. For example, understanding how populations are structured, and the sizes and demographic histories of these populations, may help us to predict how they will respond in the future and best focus our efforts where they are most effective. By including analysis of their adaptive history and responses, we may start to unravel exactly what makes a species a good invader and how to best predict future susceptibility of an environment to invasion.

Table of genetic information applications
A comprehensive table of the different ways genetic information could be applied in broader invasive species management programs, from Rollins et al. (2006). This paper specifically relates to pest management within Western Australia but the concepts listed here apply broadly. Many of these concepts we have discussed previously in a conservation management context as well.

The better we understand invasive species and populations from a genetic perspective, the more informed our management efforts can be and the more likely we are to be able to adequately address the problem.

Managing invasive pest species

The impact of human settlement into new environments is exponentially beyond our direct influences. With our arrival, particularly in the last few hundred years, human migration has been an effective conduit for the spread of ecologically-disastrous species which undermine the health and stability of ecosystems around the globe. As such, it is our responsibility to Earth to attempt to address our problems: new genetic techniques is but one growing avenue by which we might be able to remove these invasive pests.

Pressing Ctrl-Z on Life with De-extinction

Note: For some clear, interesting presentations on the topic of de-extinction, and where some of the information for this post comes from, check out this list of TED talks.

The current conservation crisis

The stark reality of conservation in the modern era epitomises the crisis discipline that so often is used to describe it: species are disappearing at an unprecedented rate, and despite our best efforts it appears that they will continue to do so. The magnitude and complexity of our impacts on the environment effectively decimates entire ecosystems (and indeed, the entire biosphere). It is thus our responsibility as ‘custodians of the planet’ (although if I had a choice, I would have sacked us as CEOs of this whole business) to attempt to prevent further extinction of our planet’s biodiversity.

Human CEO example
“….shit.”

If you’re even remotely familiar with this blog, then you would have been exposed to a number of different techniques, practices and outcomes of conservation research and its disparate sub-disciplines (e.g. population genetics, community ecology, etc.). Given the limited resources available to conserve an overwhelming number of endangered species, we attempt to prioritise our efforts towards those most in need, although there is a strong taxonomic bias underpinning them.

At least from a genetic perspective, this sometimes involves trying to understand the nature and potential of adaptation from genetic variation (as a predictor of future adaptability). Or using genetic information to inform captive breeding programs, to allow us to boost population numbers with minimal risk of inbreeding depression. Or perhaps allowing us to describe new, unidentified species which require their own set of targeted management recommendations and political legislation.

Genetic rescue

Yet another example of the use of genetics in conservation management, and one that we have previously discussed on The G-CAT, is the concept of ‘genetic rescue’. This involves actively adding new genetic material from other populations into our captive breeding programs to supplement the amount of genetic variation available for future (or even current) adaptation. While there traditionally has been some debate about the risk of outbreeding depression, genetic rescue has been shown to be an effective method for prolonging the survival of at-risk populations.

super-gene-genetic-rescue-e1549973268851.jpg
How my overactive imagination pictures ‘genetic rescue’.

There’s one catch (well, a few really) with genetic rescue: namely, that one must have other populations to ‘outbreed’ with in order add genetic variation to the captive population. But what happens if we’re too late? What if there are no other populations to supplement with, or those other populations are also too genetically depauperate to use for genetic rescue?

Believe it or not, sometimes it’s not too late to save species, even after they have gone extinct. Which brings us from this (lengthy) introduction to this week’s topic: de-extinction. Yes, we’re literally (okay, maybe not) going to raise the dead.

Necroconservaticon
Your textbook guide to de-extinction. Now banned in 47 countries.

Backbreeding: resurrection by hybridisation

You might wonder how (or even if!) this is possible. And to be frank, it’s extraordinarily difficult. However, it has to a degree been done before, in very specific circumstances. One scenario is based on breeding out a species back into existence: sometimes we refer to this as ‘backbreeding’.

This practice really only applies in a few select scenarios. One requirement for backbreeding to be possible is that hybridisation across species has to have occurred in the past, and generally to a substantial scale. This is important as it allows the genetic variation which defines one of those species to live on within the genome of its sister species even when the original ‘host’ species goes extinct. That might make absolutely zero sense as it stands, so let’s dive into this with a case study.

I’m sure you’ll recognise (at the very least, in name) these handsome fellows below: the Galápagos tortoise. They were a pinnacle in Charles Darwin’s research into the process of evolution by natural selection, and can live for so long that until recently there had been living individuals which would have been able to remember him (assuming, you know, memory loss is not a thing in tortoises. I can’t even remember what I had for dinner two days ago, to be fair). As remarkable as they are, Galápagos tortoises actually comprise 15 different species, which can be primarily determined by the shape of their shells and the islands they inhabit.

Galapagos island and tortoises
A map of the Galápagos archipelago and tortoise species, with extinct species indicated by symbology. Lonesome George was the last known living member of the Pinta Island tortoise, C. abingdonii for reference. Source: Wikipedia.

One of these species, Chelonoidis elephantopus, also known as the Floreana tortoise after their home island, went extinct over 150 years ago, likely due to hunting and tradeHowever, before they all died, some individuals were transported to another island (ironically, likely by mariners) and did the dirty with another species of tortoise: C. becki. Because of this, some of the genetic material of the extinct Floreana tortoise introgressed into the genome of the still-living C. becki. In an effort to restore an iconic species, scientists from a number of institutions attempted to do what sounds like science-fiction: breed the extinct tortoise back to life.

By carefully managing and selectively breeding captive individuals , progressive future generations of the captive population can gradually include more and more of the original extinct C. elephantopus genetic sequence within their genomes. While a 100% resurrection might not be fully possible, by the end of the process individuals with progressively higher proportion of the original Floreana tortoise genome will be born. Although maybe not a perfect replica, this ‘revived’ species is much more likely to serve a similar ecological role to the now-extinct species, and thus contribute to ecosystem stability. To this day, this is one of the closest attempts at reviving a long-dead species.

Is full de-extinction possible?

When you saw the title for this post, you were probably expecting some Jurassic Park level ‘dinosaurs walking on Earth again’ information. I know I did when I first heard the term de-extinction. Unfortunately, contemporary de-extinction practices are not that far advanced just yet, although there have been some solid attempts. Experiments conducted using the genomic DNA from the nucleus of a dead animal, and cloning it within the egg of another living member of that species has effectively cloned an animal back from the dead. This method, however, is currently limited to animals that have died recently, as the DNA degrades beyond use over time.

The same methods have been attempted for some extinct animals, which went extinct relatively recently. Experiments involving the Pyrenean ibex (bucardo) were successful in generating an embryo, but not sustaining a living organism. The bucardo died 10 minutes after birth due to a critical lung condition, as an example.

The challenges and ethics of de-extinction

One might expect that as genomic technologies improve, particularly methods facilitated by the genome-editing allowed from CRISPR/Cas-9 development, that we might one day be able to truly resurrect an extinct species. But this leads to very strongly debated topics of ethics and morality of de-extinction. If we can bring a species back from the dead, should we? What are the unexpected impacts of its revival? How will we prevent history from repeating itself, and the species simply going back extinct? In a rapidly changing world, how can we account for the differences in environment between when the species was alive and now?

Deextinction via necromancy figure
The Chaotic Neutral (?) approach to de-extinction.

There is no clear, simple answer to many of these questions. We are only scratching the surface of the possibility of de-extinction, and I expect that this debate will only accelerate with the research. One thing remains eternally true, though: it is still the distinct responsibility of humanity to prevent more extinctions in the future. Handling the growing climate change problem and the collapse of ecosystems remains a top priority for conservation science, and without a solution there will be no stable planet on which to de-extinct species.

de-extinction meme
You bet we’re gonna make a meme months after it’s gone out of popularity.